I use my inbox a lot for helping me manage certain things on my team. Revokable waiver claims, disabled list management, etc.
At the very least, I'd like to be able to toggle a message in my inbox between read / unread.
Ideally, I'd like to be able to store my messages in folders, but I think that's unlikely to happen (too much programming for a minor part of the game). So I'd settle for just being able to toggle a read message back to unread, so that I can use that as a reminder of something that I might want to take action on.